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1ak0

P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG

Method: X-RAY DIFFRACTION D_max: 60.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ak0
deposition_date	1997-05-28
title	P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG
keywords	ENDONUCLEASE, P1 NUCLEASE, REACTION MECHANISM, THIOPHOSPHORYLATED OLIGONUCLEOTIDES, GLYCOSYLATED PROTEIN; ENDONUCLEASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	19.08 Å
rg_electron	17.98 Å
i0	19031700.00
molecular_weight	30949.0 kDa
excluded_volume	37656 Å³
envelope_volume	42913 Å³
shell_volume	19564 Å³
envelope_diameter	60.9 Å
shell_rg	24.64 Å
envelope_rg	18.33 Å
shape_rg	17.98 Å
total_rg	18.86 Å
total_atoms	2159
n_residues	264
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	60.1 Å
rg_real	18.96 Å
rg_real_error	0.24 Å
i0_real	1.9030e+07
i0_real_error	1.9710e+05
rg_reciprocal	18.98 Å
i0_reciprocal	19030000.0000
total_estimate	0.8948
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.2 Å
skewness	0.181
kurtosis	-0.356
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	3264000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	P1 NUCLEASE
formula_weight	29251.0 kDa
ec_number	3.1.30.1
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2313

WGALGHATVAYVAQHYVSPEAASWAQGILGSSSSSYLASIASWADEYRLTSAGKWSASLHFIDAEDNPPTNCNVDYERDCGSSGCSISAIANYTQRVSDSSLSSENHAEALRFLVHFIGDMTQPLHDEAYAVGGNKINVTFDGYHDNLHSDWDTYMPQKLIGGHALSDAESWAKTLVQNIESGNYTAQAIGWIKGDNISEPITTATRWASDANALVCTVVMPHGAAALQTGDLYPTYYDSVIDTIELQIAKGGYRLANWINEIHGSEIAK

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 3 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	2

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	ADENOSINE-5'-(DITHIO)PHOSPHATE
formula_weight	379.4 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	THYMIDINE-5'-(DITHIO)PHOSPHATE
formula_weight	354.3 kDa
src_method	syn
entity_count	3

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	154

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6. Citations (2)

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length_a	41.980 Å
length_b	74.040 Å
length_c	102.130 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.800 Å
resolution_low	8.000 Å
r_factor	0.2070
r_work	0.2070
r_free	0.2350

fit	/app/data/saxs_computation/ak/1ak0/1ak0.fit
pddf	/app/data/pr_computation/ak/1ak0/1ak0.pr.out
profile	/app/data/saxs_computation/ak/1ak0/1ak0.dat